LAMMPS (28 Jul 2021)
  using 1 OpenMP thread(s) per MPI task
units           lj
atom_style      full
boundary p p p

special_bonds lj/coul 1 1 1
newton on on

# save an extra atom type for bond particles
read_data data.chain
Reading data file ...
  orthogonal box = (0.0000000 0.0000000 0.0000000) to (10.000000 10.000000 10.000000)
  1 by 2 by 2 MPI processor grid
  reading atoms ...
  3000 atoms
  reading velocities ...
  3000 velocities
  scanning bonds ...
  1 = max bonds/atom
  reading bonds ...
  2700 bonds
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    1        1        1       
  special bond factors coul:  1        1        1       
     2 = max # of 1-2 neighbors
     2 = max # of special neighbors
  special bonds CPU = 0.000 seconds
  read_data CPU = 0.011 seconds

neighbor        2.0 bin
neigh_modify    every 10 check yes

bond_style      harmonic
bond_coeff      * 225.0 0.85

comm_modify vel yes
comm_modify cutoff 3.6

# must use pair hybrid, since srp bond particles
# do not interact with other atoms types
pair_style      hybrid dpd 1.0 1.0 373692 srp 0.8 1 mid
pair_coeff      1 1 dpd 60.0 4.5 1.0
pair_coeff      1 2 none
pair_coeff      2 2 srp 100.0

# auto normalization of thermo quantities is turned off by pair srp
# just divide by natoms
variable        natoms equal count(all)
variable        nPotEng equal c_thermo_pe/v_natoms

thermo 50
thermo_style custom step temp pe v_nPotEng press atoms v_natoms lx ly lz

fix  1 all nve
timestep        0.01

#restart 500	mid-run-*.restart

run          1000

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- @Article{Sirk2012
 author = {T. Sirk and Y. Sliozberg and J. Brennan and M. Lisal and J. Andzelm},
 title = {An enhanced entangled polymer model for dissipative particle dynamics},
 journal = {J.~Chem.~Phys.},
 year =    2012,
 volume =  136,
 pages =   {134903}
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Using type 2 for bond particles
Thermo normalization turned off by pair srp (src/MISC/pair_srp.cpp:486)
Neighbor list info ...
  update every 10 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 3
  ghost atom cutoff = 3.6
  binsize = 1.5, bins = 7 7 7
  3 neighbor lists, perpetual/occasional/extra = 3 0 0
  (1) pair dpd, perpetual, skip from (3)
      attributes: half, newton on
      pair build: skip
      stencil: none
      bin: none
  (2) pair srp, perpetual, skip from (3)
      attributes: half, newton on
      pair build: skip
      stencil: none
      bin: none
  (3) neighbor class addition, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
Removed/inserted 0/2700 bond particles. (src/MISC/fix_srp.cpp:250)
Per MPI rank memory allocation (min/avg/max) = 10.35 | 10.35 | 10.35 Mbytes
Step Temp PotEng v_nPotEng Press Atoms v_natoms Lx Ly Lz 
       0   0.98262092    31772.336    10.590779    60.908146     5700         3000           10           10           10 
      50    1.0094645    31632.293    10.544098    61.107394     5700         3000           10           10           10 
     100    1.0067657    31633.525    10.544508    61.721089     5700         3000           10           10           10 
     150   0.99163624     31751.06    10.583687    60.437789     5700         3000           10           10           10 
     200   0.98701756    31674.754    10.558251    60.897782     5700         3000           10           10           10 
     250   0.99422545    31689.944    10.563315    61.748317     5700         3000           10           10           10 
     300   0.98351268    31756.124    10.585375    61.164735     5700         3000           10           10           10 
     350   0.99570183    31840.098    10.613366    61.210337     5700         3000           10           10           10 
     400    1.0025719    31832.008    10.610669    61.270633     5700         3000           10           10           10 
     450   0.99464256    31812.213    10.604071    60.625168     5700         3000           10           10           10 
     500   0.98753036    31822.577    10.607526    61.007786     5700         3000           10           10           10 
     550   0.98085348    31779.406    10.593135    61.268608     5700         3000           10           10           10 
     600    1.0031999    31849.695    10.616565    61.938464     5700         3000           10           10           10 
     650    1.0102644    31912.564    10.637521    61.298438     5700         3000           10           10           10 
     700    1.0238545    31799.622    10.599874    61.424427     5700         3000           10           10           10 
     750    1.0186874    31781.261    10.593754    60.706143     5700         3000           10           10           10 
     800    1.0245821    31738.473    10.579491    61.550865     5700         3000           10           10           10 
     850    1.0179726    31720.521    10.573507    61.881576     5700         3000           10           10           10 
     900    1.0154591    31760.887    10.586962    61.673156     5700         3000           10           10           10 
     950   0.99349056    31834.644    10.611548    61.624864     5700         3000           10           10           10 
    1000    1.0033121    31820.089    10.606696    60.698277     5700         3000           10           10           10 
Deleted 2700 atoms, new total = 3000
Loop time of 2.18923 on 4 procs for 1000 steps with 3000 atoms

Performance: 394659.660 tau/day, 456.782 timesteps/s
98.1% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 1.2744     | 1.2921     | 1.3222     |   1.6 | 59.02
Bond    | 0.0092027  | 0.0093722  | 0.009696   |   0.2 |  0.43
Neigh   | 0.47767    | 0.47768    | 0.47769    |   0.0 | 21.82
Comm    | 0.34932    | 0.37877    | 0.39403    |   2.9 | 17.30
Output  | 0.001045   | 0.0015711  | 0.003145   |   2.3 |  0.07
Modify  | 0.015498   | 0.016073   | 0.017271   |   0.6 |  0.73
Other   |            | 0.01362    |            |       |  0.62

Nlocal:        750.000 ave         754 max         743 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost:        6941.25 ave        6967 max        6911 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Neighs:         0.00000 ave           0 max           0 min
Histogram: 4 0 0 0 0 0 0 0 0 0

Total # of neighbors = 0
Ave neighs/atom = 0.0000000
Ave special neighs/atom = 1.8000000
Neighbor list builds = 21
Dangerous builds = 0

#write_restart   end-run.restart
Total wall time: 0:00:02
